Japan will complete the list of Scotland's autumn opponents at Murrayfield.
Gregor Townsend's side will play Australia on 7 November and world champions South Africa six days later.
The Test series concludes against Japan on 20 November.
It will be Japan's second visit to Edinburgh in 2021 as they are playing the British and Irish Lions on 26 June prior to the latter's tour to South Africa.
Scotland last met Japan at the 2019 Rugby World Cup, with the hosts winning 28-21 in Yokohama to progress to the quarter-finals.
Scotland had won all seven of the previous meetings.
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